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Yorodumi- PDB-3uxj: Crystal Structure of 7-cyano-7-deazaguanine reductase, QueF from ... -
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-Basic information
Entry | Database: PDB / ID: 3uxj | ||||||
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Title | Crystal Structure of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with NADP and PreQ0 | ||||||
Components | NADPH-dependent 7-cyano-7-deazaguanine reductase | ||||||
Keywords | Oxidoreductase/Oxidoreductase Substrate / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta structure / tunneling fold / reductase / cytosol / Oxidoreductase-Oxidoreductase Substrate complex | ||||||
Function / homology | Function and homology information preQ1 synthase / preQ1 synthase activity / queuosine biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio cholerae O1 biovar El Tor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å | ||||||
Authors | Kim, Y. / Zhang, R. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published / Year: 2012 Title: Crystal Structure of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with NADP and PreQ0 Authors: Kim, Y. / Zhang, R. / Gu, M. / Anderson, W.F. / Joachimiak, A. / CSGID | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uxj.cif.gz | 476.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uxj.ent.gz | 388 KB | Display | PDB format |
PDBx/mmJSON format | 3uxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uxj_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3uxj_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3uxj_validation.xml.gz | 54.3 KB | Display | |
Data in CIF | 3uxj_validation.cif.gz | 79.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/3uxj ftp://data.pdbj.org/pub/pdb/validation_reports/ux/3uxj | HTTPS FTP |
-Related structure data
Related structure data | 3s19S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | two dimers, chains A and B, and chains C and D. |
-Components
#1: Protein | Mass: 33271.285 Da / Num. of mol.: 4 / Mutation: R262L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria) Strain: N16961 / Gene: queF, VCM66_0859 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic References: UniProt: C3LTF1, UniProt: Q9KTK0*PLUS, preQ1 synthase #2: Chemical | ChemComp-PRF / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Nonpolymer details | THE PREQ0 COMPOUND REACTED SO THAT A COVALENT BOND WAS FORMED BETWEEN THE COMPOUND (REPRESENTED AS ...THE PREQ0 COMPOUND REACTED SO THAT A COVALENT BOND WAS FORMED BETWEEN THE COMPOUND (REPRESENTE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.73 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2 M sodium chloride, 0.1 M sodium potassium phosphate pH 6.2, 20 % (w/v) PEG-1000, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97903 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 18, 2010 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97903 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. all: 194723 / Num. obs: 194723 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 10.85 Å2 / Rsym value: 0.026 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 5 / Num. unique all: 6903 / Rsym value: 0.139 / % possible all: 67.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3S19 Resolution: 1.401→27.009 Å / SU ML: 0.17 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 14.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.887 Å2 / ksol: 0.39 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.401→27.009 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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